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Niu M, Liang X, Zhao H, Li H, Fu X, Liu C. Bipolar hemicyanine cationic probe for simultaneous sensing of ATP and GTP. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123249. [PMID: 37579665 DOI: 10.1016/j.saa.2023.123249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023]
Abstract
Adenosine 5'-triphosphate (ATP) and guanosine 5'-triphosphate (GTP) are the most essential energy source in enormous biological processes. Various probes for ATP or GTP sensing, have been widely established, but the probe that could simultaneously monitor ATP and GTP is still rarely reported. Herein, we report a bipolar hemicyanine cationic probe for simultaneous sensing of ATP and GTP via a one-step monitoring process. This probe exhibited strong affinity to ATP and GTP through intramolecular electrostatic and π-π stacking interactions, which the binding constant on each step were determined as 6.15 × 107 M-1 and 1.57 × 106 M-1 for ATP, 3.19 × 107 M-1 and 3.81 × 106 M-1 for GTP. The sensitivity and specificity of this probe toward ATP or GTP over other twelve biological analogues (adenosine 5'-diphosphate (ADP), adenosine 5'-monophosphate (AMP), guanosine 5'-diphosphate (GDP), guanosine 5'-monophosphate (GMP), Etc.) have also been successfully demonstrated. Furthermore, due to the rapid response rate (within 10 s), we also proved that this probe could be employed as a monitor tool during the ATP or GTP-related enzymatic reaction process.
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Affiliation(s)
- Mengxing Niu
- School of Applied Engineering, Henan University of Science and Technology, Sanmenxia 472000, PR China
| | - Xiaofei Liang
- School of Music, Henan University, Kaifeng 475001, PR China
| | - Haotian Zhao
- Department of Physical Education, Jiangnan University, Wuxi 214122, PR China
| | - Huixin Li
- School of Sport Science, Beijing Sport University, Beijing 100084, PR China
| | - Xuancheng Fu
- Department of Chemistry, Syracuse University, Syracuse 13244, United States.
| | - Chang Liu
- School of Sport Science, Beijing Sport University, Beijing 100084, PR China.
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2
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Middleton DA, Griffin J, Esmann M, Fedosova NU. Solid-state NMR chemical shift analysis for determining the conformation of ATP bound to Na,K-ATPase in its native membrane. RSC Adv 2023; 13:34836-34846. [PMID: 38035247 PMCID: PMC10685339 DOI: 10.1039/d3ra06236h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Structures of membrane proteins determined by X-ray crystallography and, increasingly, by cryo-electron microscopy often fail to resolve the structural details of unstable or reactive small molecular ligands in their physiological sites. This work demonstrates that 13C chemical shifts measured by magic-angle spinning (MAS) solid-state NMR (SSNMR) provide unique information on the conformation of a labile ligand in the physiological site of a functional protein in its native membrane, by exploiting freeze-trapping to stabilise the complex. We examine the ribose conformation of ATP in a high affinity complex with Na,K-ATPase (NKA), an enzyme that rapidly hydrolyses ATP to ADP and inorganic phosphate under physiological conditions. The 13C SSNMR spectrum of the frozen complex exhibits peaks from all ATP ribose carbon sites and some adenine base carbons. Comparison of experimental chemical shifts with density functional theory (DFT) calculations of ATP in different conformations and protein environments reveals that the ATP ribose ring adopts an C3'-endo (N) conformation when bound with high affinity to NKA in the E1Na state, in contrast to the C2'-endo (S) ribose conformations of ATP bound to the E2P state and AMPPCP in the E1 complex. Additional dipolar coupling-mediated measurements of H-C-C-H torsional angles are used to eliminate possible relative orientations of the ribose and adenine rings. The utilization of chemical shifts to determine membrane protein ligand conformations has been underexploited to date and here we demonstrate this approach to be a powerful tool for resolving the fine details of ligand-protein interactions.
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Affiliation(s)
- David A Middleton
- Department of Chemistry, Lancaster University Bailrigg Lancaster LA1 4YB UK +44 (0)1524 594328
| | - John Griffin
- Department of Chemistry, Lancaster University Bailrigg Lancaster LA1 4YB UK +44 (0)1524 594328
| | - Mikael Esmann
- Department of Biomedicine, Aarhus University Aarhus Denmark
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3
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Toke O. Three Decades of REDOR in Protein Science: A Solid-State NMR Technique for Distance Measurement and Spectral Editing. Int J Mol Sci 2023; 24:13637. [PMID: 37686450 PMCID: PMC10487747 DOI: 10.3390/ijms241713637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Solid-state NMR (ss-NMR) is a powerful tool to investigate noncrystallizable, poorly soluble molecular systems, such as membrane proteins, amyloids, and cell walls, in environments that closely resemble their physical sites of action. Rotational-echo double resonance (REDOR) is an ss-NMR methodology, which by reintroducing heteronuclear dipolar coupling under magic angle spinning conditions provides intramolecular and intermolecular distance restraints at the atomic level. In addition, REDOR can be exploited as a selection tool to filter spectra based on dipolar couplings. Used extensively as a spectroscopic ruler between isolated spins in site-specifically labeled systems and more recently as a building block in multidimensional ss-NMR pulse sequences allowing the simultaneous measurement of multiple distances, REDOR yields atomic-scale information on the structure and interaction of proteins. By extending REDOR to the determination of 1H-X dipolar couplings in recent years, the limit of measurable distances has reached ~15-20 Å, making it an attractive method of choice for the study of complex biomolecular assemblies. Following a methodological introduction including the most recent implementations, examples are discussed to illustrate the versatility of REDOR in the study of biological systems.
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Affiliation(s)
- Orsolya Toke
- Laboratory for NMR Spectroscopy, Structural Research Centre, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
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Shan Y, Zhang D, Luo Z, Li T, Qu H, Duan X, Jiang Y. Advances in chilling injury of postharvest fruit and vegetable: Extracellular ATP aspects. Compr Rev Food Sci Food Saf 2022; 21:4251-4273. [PMID: 35876655 DOI: 10.1111/1541-4337.13003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 01/28/2023]
Abstract
Due to the global use of cold chain, the development of postharvest technology to reduce chilling injury (CI) in postharvest fruits and vegetables during storage and transport is needed urgently. Considerable evidence shows that maintaining intracellular adenosine triphosphate (iATP) in harvested fruits and vegetables is beneficial to inhibiting CI occurrence. Extracellular ATP (eATP) is a damage-associated signal molecule and plays an important role in CI of postharvest fruits and vegetables through its receptor and subsequent signal transduction under low-temperature stress. The development of new aptasensors for the simultaneous determination of eATP level allows for better understanding of the roles of eATP in a myriad of responses mediated by low-temperature stress in relation to the chilling tolerance of postharvest fruits and vegetables. The multiple biological functions of eATP and its receptors in postharvest fruits and vegetables were attributed to interactions with reactive oxygen species (ROS) and nitric oxide (NO) in coordination with phytohormones and other signaling molecules via downstream physiological activities. The complicated interconnection among eATP in relation to its receptors, eATP/iATP homeostasis, ROS, NO, and heat shock proteins triggered by eATP recognition has been emphasized. This paper reviews recent advances in the beneficial effects of energy handling, outlines the production and homeostasis of eATP, discusses the possible mechanism of eATP and its receptors in chilling tolerance, and provides future research directions for CI in postharvest fruits and vegetables during low-temperature storage.
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Affiliation(s)
- Youxia Shan
- Guangdong Provincial Key Laboratory of Applied Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Dandan Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Taotao Li
- Guangdong Provincial Key Laboratory of Applied Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hongxia Qu
- Guangdong Provincial Key Laboratory of Applied Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Lighting up ATP in cells and tissues using a simple aptamer-based fluorescent probe. Mikrochim Acta 2021; 188:352. [PMID: 34554325 PMCID: PMC8459148 DOI: 10.1007/s00604-021-05012-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/28/2021] [Indexed: 01/02/2023]
Abstract
Extracellular ATP as a purinergic signaling molecule, together with ATP receptor, are playing an important role in tumor growth, therapy resistance, and host immunity suppression. Meanwhile ATP is a crucial indicator for cellular energy status and viability, thus a vital variable for tissue regeneration and in vitro tissue engineering. Most recent studies on COVID-19 virus suggest infection caused ATP deficit and release as a major characterization at the early stage of the disease and major causes for disease complications. Thus, imaging ATP molecule in both cellular and extracellular contexts has many applications in biology, engineering, and clinics. A sensitive and selective fluorescence “signal-on” probe for ATP detection was constructed, based on the base recognition between a black hole quencher (BHQ)-labeled aptamer oligonucleotide and a fluorophore (Cy5)-labeled reporter flare. The probe was able to detect ATP in solution with single digit µM detection limit. With the assistance of lipofectamine, this probe efficiently entered and shined in the model cells U2OS within 3 h. Further application of the probe in specific scenery, cardio-tissue engineering, was also tested where the ATP aptamer complex was able to sense cellular ATP status in a semi-quantitative manner, representing a novel approach for selection of functional cardiomyocytes for tissue engineering. At last a slight change in probe configuration in which a flexible intermolecular A14 linker was introduced granted regeneration capability. These data support the application of this probe in multiple circumstances where ATP measurement or imaging is on demand.
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Yao J, Yue T, Huang C, Wang H. A magnified aptamer fluorescence sensor based on the metal organic frameworks adsorbed DNA with enzyme catalysis amplification for ultra-sensitive determination of ATP and its logic gate operation. Bioorg Chem 2021; 114:105020. [PMID: 34328850 DOI: 10.1016/j.bioorg.2021.105020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/13/2021] [Accepted: 05/22/2021] [Indexed: 12/28/2022]
Abstract
With the development of frame materials, metal organic frameworks (MOFs) have been successfully applied in the fields of biological small molecule analysis and fluorescent DNA detection. In this work, in view of the good adsorption characteristics of MIL-101(Cr), the highly sensitive detection of adenosine triphosphate (ATP) assisted nucleic acid exonuclease amplification by MIL-101(Cr) on the different affinity of single stranded DNA and double stranded DNA was investigated. The detection limit of ATP reaches 1.7 μM, and the platform has good applicability in biological samples. On this basis, an "AND" logic gate was successfully constructed. Superior sensitivity to ATP in the presence of exonuclease was reflected, which greatly enhanced the system's fluorescence. Importantly, the fluorescence sensing application of this nanomaterial inspired other target detection and enriched the building blocks of fluorescence sensing platform.
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Affiliation(s)
- Jun Yao
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, People's Republic of China; State Key Laboratory of Oil & Gas Reservoir Geology and Exploitation, Southwest Petroleum University, Chengdu 610500, People's Republic of China.
| | - Tingting Yue
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, People's Republic of China
| | - Cheng Huang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, People's Republic of China
| | - Heng Wang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, People's Republic of China
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7
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Wang YX, Wang DX, Ma JY, Wang J, Du YC, Kong DM. DNA nanolantern-based split aptamer probes for in situ ATP imaging in living cells and lighting up mitochondria. Analyst 2021; 146:2600-2608. [PMID: 33721010 DOI: 10.1039/d1an00275a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Accurate and specific analysis of adenosine triphosphate (ATP) expression levels in living cells can provide valuable information for understanding cell metabolism, physiological activities and pathologic mechanisms. Herein, DNA nanolantern-based split aptamer nanoprobes are prepared and demonstrated to work well for in situ analysis of ATP expression in living cells. The nanoprobes, which carry multiple split aptamer units on the surface, are easily and inexpensively prepared by a "one-pot" assembly reaction of four short oligonucleotide strands. A series of characterization experiments verify that the nanoprobes have good monodispersity, strong biostability, high cell internalization efficiency, and fluorescence resonance energy transfer (FRET)-based ratiometric response to ATP in the concentration range covering the entire intracellular ATP expression level. By changing the intracellular ATP level via different treatments, the nanoprobes are demonstrated to show excellent performance in intracellular ATP expression analysis, giving a highly ATP concentration-dependent ratiometric fluorescence signal output. ATP-induced formation of large-sized DNA aggregates not only amplifies the FRET signal output, but also makes in situ ATP-imaging analysis in living cells possible. In situ responsive crosslinking of nanoprobes also makes them capable of lighting up the mitochondria of living cells. By simply changing the split aptamer sequence, the proposed DNA nanolantern-based split aptamer strategy might be easily extended to other targets.
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Affiliation(s)
- Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China.
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8
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Jiang H, Yang L, Xing X, Yan M, Guo X, Hou A, Man W, Yang B, Wang Q, Kuang H. A UPLC-MS/MS application for comparisons of the hepatotoxicity of raw and processed Xanthii Fructus by energy metabolites. RSC Adv 2019; 9:2756-2762. [PMID: 35520491 PMCID: PMC9059864 DOI: 10.1039/c8ra08272c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 01/05/2019] [Indexed: 11/21/2022] Open
Abstract
The ripe fruit of Xanthium strumarium L. (Xanthii Fructus) cannot be widely used as a Chinese herbal medicine (CHM) owing to its hepatotoxicity. However, Xanthii Fructus (XF) can be used effectively and safely after correct processing based on traditional experience, although a high hepatotoxicity risk remains owing to improper usage. Therefore, the processing methods used must be clarified to ensure safety. The adenosine-5′-triphosphate (ATP) level in tissues is an important indicator reflecting the functional status of liver cells. Therefore, this study aims to evaluate the hepatotoxicity of XF using UPLC-MS/MS. The hepatotoxicity of raw XF (RXF) and XF processed by intermediary energy metabolites (PXF) is compared. The method is evaluated for its analytical performance and successfully applied to the quantification of ATP, adenosine-5′-diphosphate (ADP), adenosine-5′-monophosphate (AMP), atractyloside, and carboxyatractyloside in mouse liver. The hepatotoxicity results also indicate that the toxicity of XF is decreased after processing, perhaps due to the decrease in atractyloside and carboxyatractyloside contents. Importantly, the experimental evidence provides a rationale for the reduction in toxicity. These data show that mouse livers are damaged between the days 20 and 30 of RXF oral administration, and that the ATP level is decreased. Importantly, no significant difference is observed between the PXF treatment group and control group, while the RXF treatment group is significantly different. Therefore, processing can reduce the toxicity of XF. The ripe fruit of Xanthium strumarium L. (Xanthii Fructus) cannot be widely used as a Chinese herbal medicine (CHM) owing to its hepatotoxicity.![]()
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Kaur H, Abreu B, Akhmetzyanov D, Lakatos-Karoly A, Soares CM, Prisner T, Glaubitz C. Unexplored Nucleotide Binding Modes for the ABC Exporter MsbA. J Am Chem Soc 2018; 140:14112-14125. [PMID: 30289253 DOI: 10.1021/jacs.8b06739] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ATP-binding cassette (ABC) transporter MsbA is an ATP-driven lipid-A flippase. It belongs to the ABC protein superfamily whose members are characterized by conserved motifs in their nucleotide binding domains (NBDs), which are responsible for ATP hydrolysis. Recently, it was found that MsbA could catalyze a reverse adenylate kinase (rAK)-like reaction in addition to ATP hydrolysis. Both reactions are connected and mediated by the same conserved NBD domains. Here, the structural foundations underlying the nucleotide binding to MsbA were therefore explored using a concerted approach based on conventional- and DNP-enhanced solid-state NMR, pulsed-EPR, and MD simulations. MsbA reconstituted into lipid bilayers was trapped in various catalytic states corresponding to intermediates of the coupled ATPase-rAK mechanism. The analysis of nucleotide-binding dependent chemical shift changes, and the detection of through-space contacts between bound nucleotides and MsbA within these states provides evidence for an additional nucleotide-binding site in close proximity to the Q-loop and the His-Switch. By replacing Mg2+ with Mn2+ and employing pulsed EPR spectroscopy, evidence is provided that this newly found nucleotide binding site does not interfere with the coordination of the required metal ion. Molecular dynamic (MD) simulations of nucleotide and metal binding required for the coupled ATPase-rAK mechanism have been used to corroborate these experimental findings and provide additional insight into nucleotide location, orientation, and possible binding modes.
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Affiliation(s)
- Hundeep Kaur
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Bárbara Abreu
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , 2780-157 Oeiras , Portugal
| | - Dmitry Akhmetzyanov
- Institute for Physical and Theoretical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Andrea Lakatos-Karoly
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Cláudio M Soares
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , 2780-157 Oeiras , Portugal
| | - Thomas Prisner
- Institute for Physical and Theoretical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance , Goethe-University Frankfurt , 60438 Frankfurt , Germany
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10
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Zhao Q, Zhang Z, Tang Y. A new conjugated polymer-based combination probe for ATP detection using a multisite-binding and FRET strategy. Chem Commun (Camb) 2018; 53:9414-9417. [PMID: 28787042 DOI: 10.1039/c7cc04293k] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new conjugated polymer-based ratiometric combination probe was constructed for adenosine triphosphate detection by taking advantage of a multisite-binding and fluorescence resonance energy transfer strategy. The method is rapid and highly selective, which can clearly discriminate ATP from persistent interferents such as ADP, AMP, other nucleoside polyphosphates and nucleobases.
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Affiliation(s)
- Qi Zhao
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, P. R. China.
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A fluorescent "on-off-on" probe for sensitive detection of ATP based on ATP displacing DNA from nanoceria. Talanta 2017; 179:285-291. [PMID: 29310233 DOI: 10.1016/j.talanta.2017.09.091] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/19/2017] [Accepted: 09/30/2017] [Indexed: 12/11/2022]
Abstract
A simple, rapid, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection was developed by using a FAM (carboxyfluorescein) labeled DNA (FAM-DNA). In this strategy, highly fluorescent FAM-DNA was used as a probe, and nanoceria (CeO2 NPs) acted as an efficient quencher. FAM-DNA attached to the surface of nanoceria through the coordination between the phosphate group of DNA and NP surface, which induced complete quenching in the FAM-DNA fluorescence due to a photo induced electron transfer (PET) process. It was found that ATP can readily displace adsorbed DNA from nanoceria surface because of the stronger coordination ability of ATP with nanoceria, and the nanoceria-based competitive binding resulted in over 7-fold fluorescence enhancement. Over a wide range from 0.1nM to 1.5μM, a good linear relationship between the fluorescence intensity and the concentration of ATP was obtained and the detection limit was estimated to be as low as 54pM. This method was successfully used to analyze ATP in a single drop of blood and human urine.
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Saidijam M, Karimi Dermani F, Sohrabi S, Patching SG. Efflux proteins at the blood-brain barrier: review and bioinformatics analysis. Xenobiotica 2017; 48:506-532. [PMID: 28481715 DOI: 10.1080/00498254.2017.1328148] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
1. Efflux proteins at the blood-brain barrier provide a mechanism for export of waste products of normal metabolism from the brain and help to maintain brain homeostasis. They also prevent entry into the brain of a wide range of potentially harmful compounds such as drugs and xenobiotics. 2. Conversely, efflux proteins also hinder delivery of therapeutic drugs to the brain and central nervous system used to treat brain tumours and neurological disorders. For bypassing efflux proteins, a comprehensive understanding of their structures, functions and molecular mechanisms is necessary, along with new strategies and technologies for delivery of drugs across the blood-brain barrier. 3. We review efflux proteins at the blood-brain barrier, classified as either ATP-binding cassette (ABC) transporters (P-gp, BCRP, MRPs) or solute carrier (SLC) transporters (OATP1A2, OATP1A4, OATP1C1, OATP2B1, OAT3, EAATs, PMAT/hENT4 and MATE1). 4. This includes information about substrate and inhibitor specificity, structural organisation and mechanism, membrane localisation, regulation of expression and activity, effects of diseases and conditions and the principal technique used for in vivo analysis of efflux protein activity: positron emission tomography (PET). 5. We also performed analyses of evolutionary relationships, membrane topologies and amino acid compositions of the proteins, and linked these to structure and function.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Fatemeh Karimi Dermani
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Sareh Sohrabi
- a Department of Molecular Medicine and Genetics , Research Centre for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences , Hamadan , Iran and
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds , UK
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15
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Middleton DA, Fedosova NU, Esmann M. Long-Range Effects of Na(+) Binding in Na,K-ATPase Reported by ATP. Biochemistry 2015; 54:7041-7. [PMID: 26538123 DOI: 10.1021/acs.biochem.5b00893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper addresses the question of long-range interactions between the intramembranous cation binding sites and the cytoplasmic nucleotide binding site of the ubiquitous ion-transporting Na,K-ATPase using (13)C cross-polarization magic-angle spinning (CP-MAS) solid-state nuclear magnetic resonance. High-affinity ATP binding is induced by the presence of Na(+) as well as of Na-like substances such as Tris(+), and these ions are equally efficient promoters of nucleotide binding. CP-MAS analysis of bound ATP with Na,K-ATPase purified from pig kidney membranes reveals subtle differences in the nucleotide interactions within the nucleotide site depending on whether Na(+) or Tris(+) is used to induce binding. Differences in chemical shifts for ATP atoms C1' and C5' observed in the presence of Na(+) or Tris(+) suggest alterations in the residues surrounding the bound nucleotide, hydrogen bonding, and/or conformation of the ribose ring. This is taken as evidence of a long-distance communication between the Na(+)-filled ion sites in the membrane interior and the nucleotide binding site in the cytoplasmic domain and reflects the first conformational change ultimately leading to phosphorylation of the enzyme. Stopped-flow fluorescence measurements with the nucleotide analogue eosin show that the dissociation rate constant for eosin is larger in Tris(+) than in Na(+), giving kinetic evidence of the difference in structural effects of Na(+) and Tris(+). According to the recent crystal structure of the E1·AlF4(-)·ADP·3Na(+) form, the coupling between the ion binding sites and the nucleotide side is mediated by, among others, the M5 helix.
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Affiliation(s)
- David A Middleton
- Department of Chemistry, B8 Faraday Building, Lancaster University , Lancaster LA1 4YB, U.K
| | - Natalya U Fedosova
- Department of Biomedicine, University of Aarhus , Ole Worms Allé 6, DK-8000 Aarhus C, Denmark
| | - Mikael Esmann
- Department of Biomedicine, University of Aarhus , Ole Worms Allé 6, DK-8000 Aarhus C, Denmark
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Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
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Xiao L, Sun S, Pei Z, Pei Y, Pang Y, Xu Y. A Ga(3+)self-assembled fluorescent probe for ATP imaging in vivo. Biosens Bioelectron 2014; 65:166-70. [PMID: 25461153 DOI: 10.1016/j.bios.2014.10.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 12/22/2022]
Abstract
Adenosine 5'-triphosphate (ATP) is a functional molecule associated with many important biological processes. Fluorescent detection methods for ATP with facile performance and high selectivity are in demand. One of the possible multi-membered arrays assembled between DHBO and Ga(3+) ions was conducted in aqueous solution, which can selectively recognize ATP with fluorescence enhancement from ADP, AMP and other structurally similar nucleoside triphosphates in vitro and in vivo. ATP facilitates the interaction between DHBO and Ga(3+) ions, resulting in the fluorescence increase. The detection limit for ATP was calculated to be 5.49×10(-7)M, which is much lower than that of intracellular concentrations (1-10mM). In addition, DHBO-Ga(3+) can be applied to detect ATP-relevant enzyme activity.
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Affiliation(s)
- Liangliang Xiao
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Shiguo Sun
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zhichao Pei
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yuxin Pei
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yi Pang
- Department of Chemistry & Maurice Morton Institute of Polymer Science, The University of Akron, Akron, OH 44325, USA
| | - Yongqian Xu
- College of Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Li X, Guo X, Cao L, Xun Z, Wang S, Li S, Li Y, Yang G. Water-soluble triarylboron compound for ATP imaging in vivo using analyte-induced finite aggregation. Angew Chem Int Ed Engl 2014; 53:7809-13. [PMID: 24909142 DOI: 10.1002/anie.201403918] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Indexed: 02/06/2023]
Abstract
Adenosine 5'-triphosphate (ATP) is a multifunctional molecule that participates in many important biological processes. Currently, fluorescence indicators for ATP with high performance are in demand. Reported herein is a novel water-soluble triarylboron compound which displays an apparent ATP-dependent fluorescence enhancement when dispersed in water. It can selectively recognize ATP from other bioactive substances in vitro and in vivo. The ATP-induced finite aggregation endows the indicator with appreciable photostability and superior tolerance to environmental electrolytes. This indicator has been successfully applied to the ATP imaging in NIH/3T3 fibroblast cells. The difference in the ATP levels within the membrane and cytosol is clearly visible.
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Affiliation(s)
- Xiaoyan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China)
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19
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Li X, Guo X, Cao L, Xun Z, Wang S, Li S, Li Y, Yang G. Water-Soluble Triarylboron Compound for ATP Imaging In Vivo Using Analyte-Induced Finite Aggregation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403918] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Goldbourt A. Biomolecular magic-angle spinning solid-state NMR: recent methods and applications. Curr Opin Biotechnol 2013; 24:705-15. [DOI: 10.1016/j.copbio.2013.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 12/28/2022]
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21
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PatchinG SG, Henderson PJF, Sharples DJ, Middleton DA. Probing the contacts of a low-affinity substrate with a membrane-embedded transport protein using1H-13C cross-polarisation magic-angle spinning solid-state NMR. Mol Membr Biol 2012; 30:129-37. [DOI: 10.3109/09687688.2012.743193] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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